builtin/apply: make apply_all_patches() return 128 or 1 on error

builtin/apply: make apply_all_patches() return 128 or 1 on error

To finish libifying the apply functionality, apply_all_patches() should not
die() or exit() in case of error, but return either 128 or 1, so that it
gives the same exit code as when die() or exit(1) is called. This way
scripts relying on the exit code don't need to be changed.

While doing that we must take care that file descriptors are properly closed
and, if needed, reset to a sensible value.

Also, according to the lockfile API, when finished with a lockfile, one
should either commit it or roll it back.

This is even more important now that the same lockfile can be passed
to init_apply_state() many times to be reused by series of calls to
the apply lib functions.

Helped-by: Nguyễn Thái Ngọc Duy <pclouds@gmail.com>
Helped-by: Johannes Schindelin <Johannes.Schindelin@gmx.de>
Helped-by: Eric Sunshine <sunshine@sunshineco.com>
Signed-off-by: Christian Couder <chriscool@tuxfamily.org>
Signed-off-by: Junio C Hamano <gitster@pobox.com>